liftOver

 

Changing genomic coordinate systems with rtracklayer::liftOver

Bioconductor version: Release (3.8)

The liftOver facilities developed in conjunction with the UCSC browser track infrastructure are available for transforming data in GRanges formats. This is illustrated here with an image of the EBI/NHGRI GWAS catalog that is, as of May 10 2017, distributed with coordinates defined by NCBI build hg38.

Author: Bioconductor Package Maintainer [aut, cre]

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Citation (from within R, enter citation("liftOver")):

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("liftOver", version = "3.8")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("liftOver")

 

HTML R Script Changing genomic coordinate systems with rtracklayer::liftOver

Details

biocViews BasicWorkflow, Workflow
Version 1.4.0
License Artistic-2.0
Depends R (>= 3.3.0), gwascat, GenomicRanges, rtracklayer, Homo.sapiens, BiocGenerics
Imports
LinkingTo
Suggests knitr, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL https://www.bioconductor.org/help/workflows/liftOver/
Depends On Me
Imports Me
Suggests Me
Links To Me

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package liftOver_1.4.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
Source Repository git clone https://git.bioconductor.org/packages/liftOver
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/liftOver
Package Short Url http://bioconductor.org/packages/liftOver/
Package Downloads Report Download Stats

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